Genocidal Genesis
by PhantomWraith
Summary: A remake of my Kage No Oni story. The original wasn't flowing like I wanted it to in the 16th chapter and it's difficult getting it to do such. I'll still be writing KNO, but it will be a little while until I update it. Thank you and enjoy the story.


Disclaimer: I do not own Naruto or Aliens

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Genocidal Genesis

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Part One: Empirical Order

Chapter One: Old Order

The first night of the year was one of a New Moon. Cloud cover was heavy and blotted out every last star in the sky. The wind howled and wailed, bearing ill news to any who will listen. The air chilled the soil and the soil chilled the water and the water chilled the Underworld.

It was a dark and terrifying night. The creatures of darkness thrived in the seemingly eternal shadows cast by the lightless sky. Any unlucky fellow caught out that night was food for them. Trees left leafless from the unnaturally harsh cold danced in the hallowing winds. Their bare branches scraped and rubbed against each other, adding the sounds of Death's violin to the voice of Hell's Lord in their undead opera.

Only one man was unafraid of his surroundings, standing fearlessly in the center of an ancient civilization. The buildings were broken and crumbling in the icy breeze, wood rotted with age and stone worn down by time. The once massive and flourishing settlement was nothing more than a great cluster of rocks and sticks piled together at the base of a great cliff in the middle of the barren forest.

Black onyx hair dancing in the wind, the man stood atop what once was and still is the tallest building in the village. Black pants tucked into black steel-toe knee-high combat boots adorned his legs, a black sleeveless turtle neck sat above a long-sleeve fishnet top, and a black sleeveless and hooded trench coat buttoned all the way up finished it off. Black elbow-length fingerless gloves with metal plating sheathed his forearms and.

"How long am I to be condemned to this barren land? How long until my sentence of banishment is lifted?" The man questioned as he turned his eyes to the sky. Irises the color of a bottomless abyss bearing dark crimson slit pupils sat in twin pools of scarlet. His eyes were lined with solid black that trailed down his cheeks, decorating his ashen flesh.

Long and sharp canines poked out from his naturally ink stained lips and black claws adorned the tips of his fingers. Standing at 6'9", he was almost 300 pounds of solid lean muscle and far more intelligent than a majority of his former peers once thought.

Just as he turned around to walk away, he saw something he hadn't seen since he came to these lands after his banishment from the Elemental Countries. It was none other than his old 'friend' and companion, who he had been forced to leave behind the day he had been kicked out of Konoha.

"Phantom? What in the nine levels of Hell are you doing here?" Naruto asked the ivory skinned and eyeless beast before him as it hissed quietly and bowed its head. Naruto narrowed his eyes in anger as he heard his companion's response. "I see. So Konoha is still trying to get their hands on my research, eh?"

Unbuttoning his trench coat and removing it, a long skeletal black tail with a barbed tip uncoiled itself from his waist and four black protrusions on his back extended out from four pre-made holes in his shirt. Folding and sealing away his coat, Naruto glanced down at Phantom before turning his eyes to the sky once more.

"They still think they can just waltz in and take whatever they want, don't they?" Naruto mumbled to himself as he took off to the northern shores of the Dead Lands. "Well, I won't let them get away with it this time without a big, bloody fight!"

Phantom gave a shrill cry of agreement as it trailed beside its master, its King, its friend. Spiked scales coated its body, giving it a heightened defense than its long-dead kin. The jagged barb on its tail made it all the more deadly than the others and its lighter and agile size gave it the advantage of speed and flexibility.

It was thanks to Naruto and his research that Phantom even came into existence. Having discovered the remains of a dead creature long ago, Naruto's curiosity and interest was sparked and ignited an inferno that became Phantom and Naruto's sought after research.

Unfortunately, Naruto's work was found out before he could continue it and was banished from Konoha for his crimes. However, no one could find his old lab or anything that might hint to where it may be. Naruto had secretly injected himself with a serum derived from the dead beast's DNA that turned him into what he was now. The creature was never before seen by anyone, leaving it nameless, but Naruto felt as if he was disrespecting it if it had no name…

Thus, he named it a Xenomorph, which roughly translates into alien form. Simple, direct, perfect. Phantom was unlike its predecessor, which was black and smooth skinned. Naruto classified the ivory Xeno as a Ghost caste and the black one as a Drone seeing as there were many exactly like it in the cavern he discovered it in.

Naruto roared in anger as he leapt off a rocky cliff overlooking the sea below, Phantom following his example.

Five Days Later

Dragging himself onto the sandy southern shores of Wave Country, Naruto took a minute to regain his breath and bearings while Phantom slowly came up beside him. The sun had yet to peek out from the horizon and the people of Wave had not quite started to stir in their beds.

They got lucky.

Five days of non-stop swimming had allowed the two to reach Wave. It was made possible for the two since Phantom had already grown used to the distance and turbulent waters on the way there and Naruto contained the Kyuubi in his body to provide near limitless stamina to keep up without even getting slightly winded.

Hissing quietly in caution, Phantom took the lead and crept up along the beach, keeping its body as close to the ground as possible. Naruto followed, confused and suspicious as to why his friend would be so paranoid and cautious when it really didn't have anything to fear.

His thoughts were cut short when his senses picked up a large number of shinobi around mid to high chuunin in strength. It was enough to give a single Xenomorph something to fear when it had no Queen Mother to lead it or other kin to aid it. Scowling upon seeing the stylized leaf symbol of Konoha on their head bands, Naruto knew he had to act fast.

"_We need to reach my lab without being spotted. Do you know if there is an underwater passage that may have opened up back when I sealed off the main entrance with explosives?"_ Naruto asked his companion through a telepathic link they had formed since Naruto had used bits and pieces of his own DNA with the Xenomorph Drone DNA to create Phantom. Unfortunately, it was only good within a fifteen mile radius and only he was able to establish it.

Phantom hissed softly in acknowledgement before turning around sharply and heading back into the water. Naruto followed closely as Phantom led him up through a nearby canal to a small four foot wide tunnel in the floor of the water way.

Taking the lead again, Phantom dove into the tunnel and weaved through the many rocks inside with its King nipping at its heels. Within a minute or two, they turned upward and broke the surface of a subterranean pool that came to a stop in yet another tunnel that split off in four directions with the pool in the center.

"Yes, yes. I know we need to develop a hive, Phantom, but we won't be able to until we can somehow acquire a Queen Mother or a suitable substitute." Naruto quietly remarked to the Ghost's nervous plea. If he were honest with himself, Naruto was nervous as well. If Konoha was able to spare nearly fifty chuunins to search for his lab in Wave Country alone, Naruto needed to get a Hive going and fast if he was going to get his revenge on Sarutobi and that damn crippled bastard.

"Hm? What do you mean by that?" Naruto inquired as Phantom hissed again. "If we can't get a Queen Mother, I'll just have to make one like I did with you. Simple as that."

Phantom gave a brief and quiet shriek as it turned and went down a tunnel to its left. Naruto blinked owlishly before glaring at his retreating creation, his eye twitching.

"Why you- I'll teach you to question my intelligence!" Naruto yelled out in annoyance as he gave chase. Phantom simply let out something akin to a shrill barking laugh as it stayed just out of Naruto's reach.

Later That Night

"Got it!" Naruto hissed to himself in excitement as he walked away from the skeletal remains of a dead Queen Mother, the same one that used to rule over the Xenomorphs in the same cave he had found over half a decade ago. He had been twelve when he found the cave and thirteen when he made Phantom, but he had been banished when Phantom, who wasn't even fully grown yet, had been spotted by a patrolling shinobi when it and Naruto were running across a street at night.

After that, everything went to Hell. The Sandaime banished him from Konoha despite being the Kyuubi jinchuuriki, labeled him as an S-class criminal in the Bingo Book, had hunter-nin track him down and try to kill him, and now the Godaime- Danzo- was after his research and searching for it with Orochimaru, his 'business' partner.

"What? No, not yet. Have patience, Phantom. We'll have a substitute Queen Mother soon enough." Naruto answered his 'pet' while returning to the laboratory section of his underground base in Wave Country. He had a piece of the Queen Mother's carapace in his hands and it should have enough DNA in it to provide a substantial quantity of serum to create a new Queen Mother.

Strapped to a pair of standing metal pillars in the middle of the lab so that her limbs formed an X was a young woman of about 16 or 17 years of age he had captured earlier that evening. Naruto had found her wandering the misty forests of Wave's south-eastern coast looking for medicinal herbs and spices. She was dressed as a civilian and hid her chakra quite well, but Naruto could tell she was at least high chuunin to low jounin in power.

"Are you sure she is adequate to become a new Queen Mother, Phantom? I mean, she's rather thin and frail looking." Naruto questioned, uncertain if the girl would suffice. Phantom hissed sharply and swiped at Naruto's head with the barbed tip of his tail. He may be Phantom's King, but they both shared the same DNA…and the same temper.

"Alright, alright! I'll get back to work. Sheesh…" Naruto grumbled as he turned around and placed the carapace fragment on a foot wide seal array meant to analyze and deconstruct any sample in it to find out what it was made of and combine needed components with other elements to stabilize the new compound. It was the same way Naruto had created the serum from the Drone DNA.

He planned on using a sample of the Queen Mother serum to change the girl, Haku, into a hybrid much like himself and to grant her similar birthing capabilities as the Queen Mother. Naruto then planned to take another sample and alter it slightly to give himself the ability to impregnate any chosen female freely with Xenomorph genetic material just in case the girl was killed or died later on.

Nearly an hour later, the process was finished. Grabbing one of the five corked vials lying in the center of the seal filled with the serum and a syringe, Naruto walked over to Haku and drew a good amount of the serum into the syringe.

"This shouldn't hurt a bit, so don't worry." Naruto assured the girl, who had awoken a few minutes after the serum extracting process began and was now frozen in fear at the sight of Phantom, unable to form words or scream or move her body in the slightest. She just kept her brown eyes locked on Naruto's face. "In fact, it should feel quite pleasurable once it starts taking effect."

She whimpered softly as the needle pierced her arm and emptied its contents into a vein. Instantly, Haku felt a sudden rush of euphoria hit her. Her pupils dilated before contracting and thinning into slits while turning silver. Then her irises and the sclera around them turned as black as night while her cream colored skin faded into a similar ashen shade as Naruto's. Her nails and canine teeth became claws and fangs identical to Naruto's and the same black markings around his eyes formed around hers. She also gained the same tail and dorsal tubes as Naruto and normal Drones.

This was expected by Naruto and Phantom, but not what came next. Almost three minutes into the transformation, Haku's figure started to change. Her small B-cup breasts swelled until they were almost G-cups from Naruto's calculations and her pelvis grew wider with plenty of meat on her hips. Her thighs grew a couple inches thicker than they were as she grew from 5'3" in height to 5'7". Her waist remained slim, but thickened slightly with muscle and balanced out her perfect hour glass figure.

Suddenly, a set of three thin horns started to protrude from her skull; one in the middle of her forehead and extending a foot up and two on the sides of her head where her temples were and going down before running parallel with her bottom jaw and stopping about three inches in front of her chin.

"Did you know this would happen, Phantom?" Naruto asked his ivory skinned friend without taking his eyes off Haku. Phantom just shook its head, silent. Remembering how the old Queen Mother was positioned, Naruto got an idea.

"Hey…Doesn't a Queen Mother need a large enclosed space with humid conditions for the eggs to survive, right?" He asked the Ghost beside him, who hissed in reply. "Ok, well…We'll need to move her somewhere with those proper conditions. Fortunately, I had been working on expanding my laboratory the year before I created you, but didn't get far due to lack of resources and man power. So long as she doesn't start laying any eggs or anything, it should do until we can get it finished."

Phantom hissed again in agreement before facing the altered Haku and slowly creeping towards her in a hesitant manner on all fours. Sluggishly and drowsily, Haku looked down at Phantom and gave it a soft smile before using her tail to brush it against the Ghost's neck and cheek tenderly.

"Hello there, young one." Haku whispered softly, still smiling warmly at the eyeless creature before her. As Phantom nuzzled her hip and side, Naruto started grinning viciously, knowing the serum had worked perfectly. Not only did it completely alter the girl's DNA and biology, but also her mind and behavioral patterns.

Before the transformation, Haku was deathly afraid of him and Phantom, but now her personality was more maternal and motherly. It was quite interesting to him, but he planned on altering a sample of the serum soon to do as he planned. Plus, with a fully-intact Queen Mother skeleton, Naruto had enough genetic material to make hundreds of new hybrid Queen Mothers if he needed to.

Not that he would; it would create too much conflict within his Hive.

Undoing the straps on her ankles and wrists, Naruto picked up the drowsy and tired Haku bridal style and carried her towards the incomplete section of his base. Once there, he placed her down on an old cot he had left behind for when he worked well into the night on enlarging the new cavern.

As he turned to walk away, Haku's tail found itself wrapped around Naruto's wrist as Haku herself curled up into a ball and started sucking on her thumb, oddly enough, as she fell asleep. Smiling slightly at the sight, Naruto found her to be quite cute and adorable at the moment. He took a moment to free his wrist before unsealing his trench coat and covering Haku with it.

"Sleep well, Haku. You'll need all the rest you can get once your duties as a Queen Mother start." Naruto whispered into her ear as he leaned down to kiss Haku on the side of her head. It was a bit of a challenge due to her horns, but he managed. How much the Queen Mother DNA will change her over a long period of time, Naruto didn't know.

Dismissing it with an exasperated sigh, he turned away with Phantom at his side and started channeling his Earth chakra to make it easier to clear out sections of the chamber.

Three Weeks Later

Hyuuga Hinata frowned slightly as she looked forward at the glowing horizon ahead of her, wishing she could see her old crush again. Her team mates Inuzuka Kiba and Aburame Shino were walking beside her as they continued on their way to a small island nation off of Fire Country's south eastern coast, Wave Country, to relieve a team of ill chuunin.

Her crush, Naruto, had been banished before she could build up the courage to confess her feelings for him. Ergo, she lost her one chance of true happiness. Where other people saw the dead-last loser of the class and a pathetic excuse of a ninja, Hinata saw a smart boy her age that was far more determined and head strong than any other person in the world. Where others saw a demon and a criminal, she saw only a misunderstood human and a man whose actions were misinterpreted.

Her last memory of him was when Naruto fled Konoha with that white creature while trading ninjutsu techniques with a team of pursuing jounin. She was never told why he really left, only that he committed some sort of serious crime and was banished because of it.

"Holy shit! What the hell happened here?" Exclaimed Kiba as he ran a short distance ahead for a slightly better view. Shino and Hinata were at his side in a moment and could only stare in shock and awe of the chaos that now engulfed Wave Country.

In the dying light of dusk, the scattered fires glowed menacingly. Ninjutsu techniques of various elements were being shot off all over the island nation and even from where they stood, Team 8 could hear the cries of pain and death from shinobi and the shrill high-pitched shrieks of unknown entities battling with the shinobi.

"Damn it! What the hell is going on here?" Kiba growled as did Akamaru. Shino's Kikaichu were buzzing loudly, but only the Aburame understood why. They were afraid. They knew what was causing such a calamity, but they wouldn't say what it was. It made Shino nervous since his colony never held back any information, especially not critical information such as the beings attacking Wave Country.

"We have to help them!" Kiba declared as he moved to charge across the bridge connecting Wave and Fire Country, but Shino grabbed his arm and held him back.

"Wait. We have no knowledge of what is going on and we'll only get ourselves hurt or killed." Shino calmly explained, though he still felt more nervous than a long tailed cat in a room full of rocking chairs.

"S-Shino-kun's right, Kiba-kun. We should think about how we'll do this." Hinata quietly added in, hoping Shino knew what he was talking about. Before Shino could open his mouth to explain his theory and plan, a pair of hisses and a set of footsteps sounded off from behind them.

Spinning around with kunai in their hands, Team 8 was greeted with the eyeless faces of two pitch black creatures and someone the two males of the chuunin team didn't recognize. Hinata, however, remembered the man's face.

"…Naruto-kun…" She whispered, tears of joy and confusion welling up in the corners of her eyes. Shino and Kiba heard her and were instantly on edge, their muscles tense and ready for combat. Unlike their timid comrade, they had heard of what Naruto had done, but Kiba was the only one sickened by it.

"Naruto, you bastard! What the hell do you think you're doing?" Kiba growled angrily while Akamaru lowered his head and tail, slowly backing up a couple steps. He knew what those things were; the elder canines whispered of them every once in awhile to the pups, warning them of the black demonic serpents and to run away no matter what if they see one.

"I'm simply getting my revenge on Konoha after what they did to me." The tailed man of 18 years replied with a blank expression. "As for any critical details, I'm not as stupid as you believe me to be, foolish Inuzuka."

"Then I'll MAKE you talk!" Kiba snarled and prepared to lunge at the stoic man before him.

"Don't you move, Kiba!" Hinata yelled out, surprising everyone present since she rarely ever raised her voice to anyone. "I swear to Kami, if you move, I'll kill you myself!"

"Oh? What is this?" Naruto muttered quietly to himself as Hinata turned her attention and kunai on her long time friend and team mate. He remembered the girl vaguely from when he was still living in Konoha, but not much else. For her to be defending him, Naruto something serious was going on since no one ever defended him throughout his entire life.

"H-Hinata? What the hell are you doing? He's the enemy! An S-class criminal!" Kiba tried to explain to her, but his words fell on deaf ears. "Back in Konoha, he _killed_ dozens of people, _innocent_ people, to create those…those _things_ over there!"

"Heh…" Naruto shook his head slightly as a grin formed on his face, the attention of the others having been turned to him. "You really think those people were innocent, don't you, foolish Inuzuka?"

"Hell yeah, I do!"

"Then you're a damn fool!" Naruto snapped, his anger and fury made obvious. Kiba flinched back in fear, his bravado forgotten. "Those _people_ were responsible for half of Konoha's problems. Thirty of them were former Civilian Council members that had made it their goal in life to hike up taxes and pocket it all for their own benefit. Fifty-nine of them were hit-men hired by the current and previous Civilian Council to kill certain politicians and other people of different countries just to keep Konoha on top. Besides, I wouldn't waste my time spawning any of my pets with those vile husks of wasted flesh."

"You're ly-!" Kiba tried to cut in as Naruto paused for a breath. Shino was smart enough to keep quiet through the whole thing and Hinata was still focused on following through with her threat on Kiba's life.

"SILENCE!" Naruto barked out, fangs bared. "Your Godaime Hokage is responsible for more than eighty percent of Konoha's problems all because he wasn't chosen to become the Sandaime Hokage all those years ago. Danzo's Root, although disbanded by the Sandaime, was and still is around to act as his private security force. Every department of ANBU, every rank, every shinobi job has at least five Root operatives spying on everyone in Konoha's ranks."

There was a pregnant pause as Naruto let it all sink in. Kiba was wise enough to stay quiet during this tense moment. Naruto then turned his eyes to Shino.

"Isn't that right, Aburame Shino? Or should I call you by your given call sign, the King Scorpion?" Naruto inquired with narrowed eyes and a dark grin. Shino was instantly on edge and slowly started to back up so a triangle was formed between him, his team mates, and Naruto. "Ah. It seems I hit the nail right on the head. Right, King Scorpion?"

"What is he talking about, Shino?"Hinata asked hesitantly. Shino, as Naruto predicted, didn't answer her question.

"How long have you known, Naruto?" The Aburame asked, eyes narrowed slightly behind his sunglasses. His insects still wouldn't obey him, not even the small number of scorpions hidden inside his trench coat and body.

"Since the first day we met in the Academy. I've had my share of run-ins with Root operatives before and I knew the signs of one well enough to pick them out of large crowds instantly." He explained before snapping his fingers. On cue, Phantom and two other Drones shot out of the shadows and tackled Shino to the ground. The Drones held the Aburame's arms and legs down while Phantom kept its clawed hands on Shino's head and jaw to keep the young man from biting down on the poison casing in his tooth.

"Nice try, though." Naruto praised the bug user before turning back to Kiba and Hinata. "Now, this is usually where the villain finishes his monologue by gloating about how he had won and divulging his plans to the captured hero. However, I'm not that arrogant or stupid. I'm going to offer you two a position in my Hive. If you don't take my offer, I'll either kill you now or let you find out how I spawn new Drones."

It was silent for several minutes before one of them spoke up. It was Kiba, of all people.

"I accept your offer." The Inuzuka replied as he dropped his kunai and bowed his head, surprising Naruto a little.

"So quick to change sides, huh? How do I know you won't betray me farther on down the road?"

That was when Kiba did something no one expected. He picked up his dropped kunai, chose his target…

And threw the kunai…

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